docs: regenerate CLI command reference from Deno 2.9.0#3357
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The new 2.9 subcommands (
deno list,deno watch,deno link,deno unlink)shipped with placeholder entries in the autogenerated CLI command reference, so
their pages rendered without a flag/options table. This regenerates
runtime/reference/cli/_commands_reference.jsonfrom Deno 2.9.0 withdeno json_reference(the same command the version-bump workflow uses), fillingin the real flags for those subcommands and refreshing the rest of the reference
to match the released CLI.